Recommendation of Tahiti acid lime cultivars through Bayesian probability models

Probabilistic models enhance breeding, especially for the Tahiti acid lime, a fruit essential to fresh markets and industry. These models identify superior and persistent individuals using probability theory, providing a measure of uncertainty that can aid the recommendation. The objective of our study was to evaluate the use of a Bayesian probabilistic model for the recommendation of superior and persistent genotypes of Tahiti acid lime evaluated in 12 harvests. Leveraging the Monte Carlo Hamiltonian sampling algorithm, we calculated the probability of superior performance (superior genotypic value), and the probability of superior stability (reduced variance of the genotype-by-harvests interaction) of each genotype. The probability of superior stability was compared to a measure of persistence estimated from genotypic values predicted using a frequentist model. Our results demonstrated the applicability and advantages of the Bayesian probabilistic model, yielding similar parameters to those of the frequentist model, while providing further information about the probabilities associated with genotype performance and stability. Genotypes G15, G4, G18, and G11 emerged as the most superior in performance, whereas G24, G7, G13, and G3 were identified as the most stable. This study highlights the usefulness of Bayesian probabilistic models in the fruit trees cultivars recommendation.

The authors are grateful for this observation from the Editor.A second check on the provided links was conducted, and a few changes were made, e.g., titles of captions and figures were bolded, and minor alterations were made to the acknowledgments.Other than that, everything is in accordance with the established norms.Changes are highlighted in blue in the Manuscript.
2. In your Methods section, please provide additional information regarding the permits you obtained for the work.Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why.
Thank you for this observation.We have added more information about the location of the experiment.This partnership does not present any conflict of interest, and there is no formal documentation regarding it.The company provides the site for carrying out the experiment and labor for managing the plants.In return, the university can generate fruit cultivation information for all the farmers in the region, without any right to exclusivity, and the transference of information takes place through the execution of field days held on the Bello Fruit farm.
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Thank you and sorry for this misunderstanding.We have revised the Acknowledgments section, removing any issues of funding.However, we reiterate the need to disclose this information as funding agencies commonly require acknowledgment of their contributions in papers and abstracts.We added the information previously contained in the Acknowledgments to the cover letter (file named "cover_letter_financial_disclosure_changes.pdf")so that it may be placed in the appropriate section on the published paper.We note that you have provided funding information that is not currently declared in your Funding Statement.However, funding information should not appear in the Acknowledgments section or other areas of your manuscript.We will only publish funding information present in the Funding Statement section of the online submission form.
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Thank you for the observation.As this point is related to the previous matter, it has already been addressed with the modifications mentioned in topic 3. We have modified the Acknowledgments section and have moved the paragraph mentioning the Funding information to the cover letter (file named "cover_letter_financial_disclosure_changes.pdf")so that it may be placed in the appropriate section on the published paper.
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We appreciate the comment and have now added the complete dataset that was used for the analyses to GitHub repository with public access.Consequently, we have inserted the link in the Supporting Information section.All authors of the manuscript have agreed to publish the full dataset to the scientific community.
The link to access the dataset is: https://github.com/malikouskirg/PONE-D-23-384846. Please review your reference list to ensure that it is complete and correct.If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript.If you need to cite a retracted article, indicate the article's retracted status in the References list and also include a citation and full reference for the retraction notice.
Thank you for the information; we have reviewed the reference list, and everything is in accordance with the standards.

Reviewer #1
• Optimization of Tahiti Acid Lime Cultivars Recommendation Through Probability Concepts Thank you for your observation.We believe that the name suggestion given by the reviewer is very relevant.We like the idea of adding the term "Bayesian" term to the title.We made a small adjustment to the reviewer's idea.Thus, the new title is " Recommendation of 'Tahiti' acid lime cultivars through Bayesian probability models".
• Tahiti Acid Lime Breeding Thank you for the suggestion.We adopted this short title.

• any breeding program
We made the recommend.Thank you.

• a
Thank you, we add the letter "a" in the sentence "The objective of our study was to evaluate the use of a Bayesian probabilistic model".
• The objective of our study was to evaluate the use of Bayesian probabilistic models for the recommendation of superior and persistent genotypes of 'Tahiti' acid lime evaluated in 12 harvests.Thank you for your suggestion.We have removed the "s" from the word "models." However, we believe that keeping the word "persistent" would be important, as in addition to performance, the objective of this work was also focused on persistence.
Thank you for your suggestion.However, we believe that this information is very important in practical terms, as it concerns the recommendation of genotypes.We have provided details about the coding in the Methods section, and therefore, the authors feel it is better to retain this information.

• Usefulness
Thank you, we changed for the suggested word.

• the fruit trees cultivars recommendation
We made the recommend change.Thank you.
• In the presence of complex GHI, breeders must consider the productivity and the stability of the genotypes over harvests [3][4][5].
We made the recommend change.Thank you.
• To address the common issue of non-orthogonal longitudinal data, resulting from the interdependence….Despite considerable progress in 'Tahiti' acid lime breeding, straightforward methodologies for exploring GHI and identifying high performance and stable genotypes are yet to be established.
Thank you for the suggestion.We removed these parts of the text.
• optimize the Tahiti acid lime cultivars recommendation, since it uses probability concepts.
We made the recommend change.Thank you.
• Dias et al. [10] proposed to use probability concepts from Bayesian models to assist in the selection of genotypes that gather favorable alleles for performance and stability across environments.
We appreciate your suggestion and have adopted it in part, as retaining the information on alleles favorable for performance and stability is relevant.This is the genetic definition of the GHI interaction; thus, the text has been revised accordingly.
" Dias et al. [11] proposed to use Bayesian probability concepts to assist in the selection of genotypes that gather favorable alleles for performance and stability across environments and harvesters." • This methodology has been proposed for the multiple location context.
Nevertheless, we believe that the same ideas are valid for the multi-harvest scenario Thank you for the suggestion.We removed these parts of the text.
• The objective of our study was to evaluate the use of a Bayesian probabilistic model for the recommendation of superior and persistent genotypes of Tahiti acid lime evaluated in 12 harvests.
Thank you.We have adopted your suggested objective.
• statistical Thank you.We added this part to the manuscript.

• was
We made the recommend change.Thank you.

• Codes
We made the recommend change.Thank you.

• method
We made the recommend change.Thank you.
• How the permanent environmental effect was accounted here?Based on the results presented in Table 3, it seems that this effect was fitted, however it was not described here.
We appreciate the comment and apologize for the oversight.Indeed, there is a permanent environmental effect, which we have now correctly included in the model.With this adjustment, we identified values in the table that were switched.
We revised the notations.
• We used a Monte Carlo Hamiltonian algorithm (the Hamiltonian Monte Carlo algorithm) in four Markov chains with 4000 samples (thin?) and 50% burn-in.Thank you for the observation; we have revised the text to "the Hamiltonian Monte Carlo algorithm" and have added the thinning information of the model, which in this case was the default of the "rstan" package, 1.
• Package Thank you.We changed the word "software" to "package".
• Proportion Thank you.We changed the word "intensity" to "proportion".
• Effects Thank you.We changed the word "effect" to "effects".
• Was.. Were Thank you.We changed the words "is/are" to "was/were".
• Comparative statistics of Bayesian models using the 'Tahiti' acid file dataset.
Thank you for the suggestion; we have removed the term "using the Tahiti acid file dataset" from all captions, table titles, and figures where this text appeared.
• 'Tahiti' Thank you for your observation.In scientific articles, the word "Tahiti" is found both with and without quotation marks.Following the reviewer's suggestion, and after grammatical research, we decided to adopt the reviewer's advice to remove the quotation marks from the name Tahiti, resulting in 'Tahiti lime'.We have carried out the removal throughout the text.
• is the genotypes-by-harvesters interaction… is the variance of the environmental permanent effect Thank you for the suggestion.We have changed the caption of Table 3 to the form proposed by the reviewer.
• by Thank you.We changed the word "in" to "by".
• important Thank you.We changed the word "informative" to "important".
• genetic evaluation Thank you.We changed the word "assessment" to "genetic evaluation".
• with heterogeneous residuals Thank you.We changed the word "heterogeneous model" to "heterogeneous residuals model".
• repeated measures Thank you.We changed the word "longitudinal" to "repeated measures".
• [https://doi.org/10.1007/s11295-023-01596-9]Thank you.We have added this citation in the mentioned part of the text, as well as in the references.
• By applying probabilistic Bayesian models in longitudinal `Tahiti` acid lime dataset Thank you.We have removed the terms "longitudinal" and "dataset" from the conclusion, as well as the previously mentioned quotation marks from 'Tahiti' throughout the text.
• This information is irrelevant to the reader.
As previously mentioned, the authors believe that maintaining the information about the recommended genotypes regarding performance and persistence is important in practical terms, since these materials are publicly available to farmers.This work, in addition to its statistical nature, is also aimed at assisting in the recommendation for planting of the Tahiti acid lime.